The bond distances in 2-cyano-
N-(2,6-dimethoxypyrimidin-4-yl)-3-[4-(dimethylamino)phenyl]acrylamide, C
18H
19N
5O
3, (I), and in the anionic component of the salt dimethylammonium 6-cyano-1,3-dimethyl-2,4,5-trioxo-1,2,3,4,5,8-hexahydropyrido[2,3-
d]pyrimidin-8-ide, C
2H
8N
2+·C
10H
7N
4O
3−, (II), provide evidence for the occurrence of electronic polarization. There are no hydrogen bonds in the structure of (I), instead pairs of molecules are linked into centrosymmetric dimers by a single π–π stacking interaction. In (II), a combination of a two-centre N—H
O hydrogen bond, a three-centre N—H
(O)
2 hydrogen bond, together utilizing all three O atoms, and a two-centre C—H
N hydrogen bond, link the components into a ribbon containing
R12(6),
R22(10) and
R66(30) rings.
Supporting information
CCDC references: 765479; 765480
For the synthesis of (I), a solution of
2-cyano-N-(2,6-dimethoxypyrimidin-4-yl)acetamide (1.0 mmol) and
4-(N,N-dimethylamino)benzaldehyde (1.0 mmol) in ethanol (10 ml)
containing a catalytic quantity of sodium hydroxide (20% w/v
aqueous solution, 5 drops) was stirred for 3 h at ambient temperature. The
resulting precipitate was collected by filtration, washed with ethanol, and
recrystallized from a mixture of dimethylformamide and ethanol to give yellow
crystals of (I) suitable for single-crystal X-ray diffraction (yield 76%, m.p.
526–527 K). Analysis: MS (70 eV): 354 (17), 353 (76, M+), 352 (16),
199 (65), 182 (100), 172 (20), 171 (58), 156 (12).
For the synthesis of (II), a solution of
3-(6-amino-1,2,3,4-tetrahydro-1,3-dimethyl-2,4-
dioxopyrimidin-5-yl)-3-oxo-propanenitrile (1.9 mmol) and dimethylformamide
dimethyacetal (3.0 mmol) in toluene (5.3 ml) was heated at 393 K for 30 min.
The resulting solid product was collected by filtration, washed and
recrystallized from ethanol to give yellow crystals of (II) suitable for
single-crystal X-ray diffraction (yield 70%, m.p. 532–534 K). Analysis: MS
(70 eV) 232 [M+ - 45 (HN(CH3)2] (37); 204 (12); 120 (35).
All H atoms were located in difference maps and then treated as riding atoms in
geometrically idealized positions, with C—H = 0.98 (methyl) or 0.95 Å
(aromatic, heteroaromatic and alkenyl) and N—H = 0.88 (N—H) or 0.92 Å
(NH2), and with Uiso(H) = kUeq(carrier), where k =
1.5 for the methyl groups, which were permitted to rotate but not to tilt, and
1.2 for all other H atoms.
For both compounds, data collection: COLLECT (Nonius, 1999); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).
(I) 2-cyano-
N-(2,6-dimethoxypyrimidin-4-yl)-3-[4-
(dimethylamino)phenyl]acrylamide
top
Crystal data top
C18H19N5O3 | Z = 2 |
Mr = 353.38 | F(000) = 372 |
Triclinic, P1 | Dx = 1.381 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 7.9772 (2) Å | Cell parameters from 3350 reflections |
b = 10.0023 (4) Å | θ = 3.1–26.1° |
c = 10.8409 (5) Å | µ = 0.10 mm−1 |
α = 93.693 (2)° | T = 120 K |
β = 93.562 (3)° | Needle, yellow |
γ = 99.196 (2)° | 0.23 × 0.12 × 0.12 mm |
V = 849.80 (6) Å3 | |
Data collection top
Bruker Nonius KappaCCD area-detector diffractometer | 3350 independent reflections |
Radiation source: Bruker Nonius FR591 rotating anode | 2512 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.055 |
Detector resolution: 9.091 pixels mm-1 | θmax = 26.1°, θmin = 3.1° |
ϕ and ω scans | h = −9→9 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −12→12 |
Tmin = 0.978, Tmax = 0.988 | l = −13→13 |
15270 measured reflections | |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.047 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.133 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0813P)2 + 0.0098P] where P = (Fo2 + 2Fc2)/3 |
3350 reflections | (Δ/σ)max = 0.001 |
239 parameters | Δρmax = 0.30 e Å−3 |
0 restraints | Δρmin = −0.28 e Å−3 |
Crystal data top
C18H19N5O3 | γ = 99.196 (2)° |
Mr = 353.38 | V = 849.80 (6) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.9772 (2) Å | Mo Kα radiation |
b = 10.0023 (4) Å | µ = 0.10 mm−1 |
c = 10.8409 (5) Å | T = 120 K |
α = 93.693 (2)° | 0.23 × 0.12 × 0.12 mm |
β = 93.562 (3)° | |
Data collection top
Bruker Nonius KappaCCD area-detector diffractometer | 3350 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 2512 reflections with I > 2σ(I) |
Tmin = 0.978, Tmax = 0.988 | Rint = 0.055 |
15270 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.047 | 0 restraints |
wR(F2) = 0.133 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.30 e Å−3 |
3350 reflections | Δρmin = −0.28 e Å−3 |
239 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.61431 (15) | 0.17404 (13) | 0.88150 (12) | 0.0168 (3) | |
C2 | 0.54750 (18) | 0.10950 (15) | 0.77337 (14) | 0.0166 (3) | |
N3 | 0.46465 (15) | 0.15698 (12) | 0.68130 (12) | 0.0172 (3) | |
C4 | 0.44916 (18) | 0.29010 (15) | 0.69915 (14) | 0.0162 (3) | |
C5 | 0.51551 (17) | 0.37031 (15) | 0.80405 (14) | 0.0168 (3) | |
H5 | 0.5071 | 0.4640 | 0.8147 | 0.020* | |
C6 | 0.59629 (18) | 0.30358 (15) | 0.89377 (14) | 0.0163 (3) | |
O2 | 0.56916 (13) | −0.02176 (10) | 0.76471 (10) | 0.0212 (3) | |
C21 | 0.5067 (2) | −0.10007 (17) | 0.65065 (16) | 0.0280 (4) | |
H21A | 0.3851 | −0.0972 | 0.6347 | 0.042* | |
H21B | 0.5234 | −0.1944 | 0.6571 | 0.042* | |
H21C | 0.5691 | −0.0620 | 0.5824 | 0.042* | |
O6 | 0.65606 (13) | 0.37715 (10) | 1.00031 (10) | 0.0201 (3) | |
C61 | 0.7247 (2) | 0.30378 (16) | 1.09691 (15) | 0.0225 (4) | |
H61A | 0.6419 | 0.2235 | 1.1104 | 0.034* | |
H61B | 0.7484 | 0.3628 | 1.1738 | 0.034* | |
H61C | 0.8304 | 0.2753 | 1.0720 | 0.034* | |
N41 | 0.35598 (15) | 0.33326 (13) | 0.60046 (12) | 0.0171 (3) | |
H41 | 0.3040 | 0.2693 | 0.5452 | 0.020* | |
C42 | 0.33595 (18) | 0.46381 (15) | 0.57948 (14) | 0.0169 (3) | |
O42 | 0.40720 (14) | 0.56194 (11) | 0.64753 (10) | 0.0229 (3) | |
C43 | 0.22379 (18) | 0.48007 (16) | 0.46827 (14) | 0.0169 (3) | |
C44 | 0.14629 (19) | 0.36036 (16) | 0.39376 (15) | 0.0202 (4) | |
N44 | 0.08482 (18) | 0.25996 (15) | 0.33940 (13) | 0.0297 (4) | |
C45 | 0.19902 (18) | 0.60817 (16) | 0.44639 (14) | 0.0174 (4) | |
H45 | 0.2546 | 0.6756 | 0.5076 | 0.021* | |
C51 | 0.10538 (18) | 0.66115 (15) | 0.34888 (15) | 0.0175 (3) | |
C52 | 0.03099 (18) | 0.58625 (16) | 0.23900 (15) | 0.0193 (4) | |
H52 | 0.0411 | 0.4931 | 0.2267 | 0.023* | |
C53 | −0.05580 (18) | 0.64474 (16) | 0.14934 (15) | 0.0191 (4) | |
H53 | −0.1047 | 0.5913 | 0.0765 | 0.023* | |
C54 | −0.07375 (18) | 0.78354 (16) | 0.16357 (15) | 0.0178 (4) | |
C55 | 0.00235 (18) | 0.86011 (16) | 0.27247 (15) | 0.0195 (4) | |
H55 | −0.0064 | 0.9536 | 0.2846 | 0.023* | |
C56 | 0.08905 (19) | 0.79964 (16) | 0.36099 (15) | 0.0193 (4) | |
H56 | 0.1400 | 0.8533 | 0.4332 | 0.023* | |
N54 | −0.16249 (16) | 0.84038 (14) | 0.07516 (13) | 0.0216 (3) | |
C57 | −0.2340 (2) | 0.76240 (18) | −0.03952 (15) | 0.0251 (4) | |
H57A | −0.1416 | 0.7372 | −0.0869 | 0.038* | |
H57B | −0.2998 | 0.8176 | −0.0888 | 0.038* | |
H57C | −0.3088 | 0.6800 | −0.0200 | 0.038* | |
C58 | −0.1775 (2) | 0.98365 (16) | 0.08968 (16) | 0.0249 (4) | |
H58A | −0.2332 | 1.0014 | 0.1657 | 0.037* | |
H58B | −0.2456 | 1.0070 | 0.0183 | 0.037* | |
H58C | −0.0638 | 1.0389 | 0.0948 | 0.037* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0185 (7) | 0.0153 (7) | 0.0168 (7) | 0.0031 (5) | 0.0006 (5) | 0.0017 (5) |
C2 | 0.0178 (8) | 0.0152 (8) | 0.0175 (8) | 0.0036 (6) | 0.0028 (6) | 0.0034 (6) |
N3 | 0.0199 (7) | 0.0139 (7) | 0.0182 (7) | 0.0041 (5) | 0.0011 (5) | 0.0017 (5) |
C4 | 0.0147 (7) | 0.0165 (8) | 0.0179 (8) | 0.0029 (6) | 0.0033 (6) | 0.0027 (6) |
C5 | 0.0174 (8) | 0.0134 (8) | 0.0200 (8) | 0.0039 (6) | 0.0016 (6) | 0.0011 (6) |
C6 | 0.0161 (7) | 0.0162 (8) | 0.0162 (8) | 0.0013 (6) | 0.0012 (6) | 0.0001 (6) |
O2 | 0.0311 (6) | 0.0125 (6) | 0.0201 (6) | 0.0064 (4) | −0.0030 (5) | 0.0002 (5) |
C21 | 0.0457 (10) | 0.0161 (9) | 0.0216 (9) | 0.0082 (7) | −0.0055 (8) | −0.0033 (7) |
O6 | 0.0259 (6) | 0.0162 (6) | 0.0178 (6) | 0.0052 (4) | −0.0049 (5) | −0.0009 (5) |
C61 | 0.0288 (9) | 0.0211 (9) | 0.0176 (9) | 0.0063 (7) | −0.0052 (7) | 0.0026 (7) |
N41 | 0.0195 (7) | 0.0146 (7) | 0.0168 (7) | 0.0037 (5) | −0.0032 (5) | 0.0014 (5) |
C42 | 0.0184 (8) | 0.0167 (8) | 0.0166 (8) | 0.0036 (6) | 0.0044 (6) | 0.0031 (7) |
O42 | 0.0296 (6) | 0.0160 (6) | 0.0221 (6) | 0.0036 (5) | −0.0057 (5) | 0.0014 (5) |
C43 | 0.0170 (8) | 0.0173 (8) | 0.0166 (8) | 0.0029 (6) | 0.0012 (6) | 0.0022 (6) |
C44 | 0.0238 (8) | 0.0201 (9) | 0.0184 (8) | 0.0076 (7) | −0.0003 (7) | 0.0060 (7) |
N44 | 0.0422 (9) | 0.0228 (8) | 0.0231 (8) | 0.0058 (7) | −0.0052 (7) | 0.0005 (7) |
C45 | 0.0166 (7) | 0.0177 (8) | 0.0178 (8) | 0.0024 (6) | 0.0017 (6) | 0.0015 (6) |
C51 | 0.0148 (7) | 0.0173 (8) | 0.0203 (8) | 0.0012 (6) | 0.0024 (6) | 0.0026 (7) |
C52 | 0.0211 (8) | 0.0146 (8) | 0.0223 (9) | 0.0036 (6) | 0.0006 (6) | 0.0025 (7) |
C53 | 0.0188 (8) | 0.0192 (9) | 0.0184 (8) | 0.0009 (6) | −0.0008 (6) | 0.0011 (7) |
C54 | 0.0147 (7) | 0.0180 (9) | 0.0214 (9) | 0.0027 (6) | 0.0022 (6) | 0.0064 (7) |
C55 | 0.0196 (8) | 0.0145 (8) | 0.0246 (9) | 0.0034 (6) | 0.0021 (6) | 0.0018 (7) |
C56 | 0.0195 (8) | 0.0182 (8) | 0.0195 (9) | 0.0013 (6) | 0.0001 (6) | 0.0012 (6) |
N54 | 0.0232 (7) | 0.0206 (7) | 0.0220 (8) | 0.0059 (6) | −0.0016 (6) | 0.0058 (6) |
C57 | 0.0242 (8) | 0.0292 (10) | 0.0228 (9) | 0.0068 (7) | −0.0021 (7) | 0.0067 (7) |
C58 | 0.0270 (9) | 0.0217 (9) | 0.0282 (10) | 0.0088 (7) | 0.0006 (7) | 0.0093 (7) |
Geometric parameters (Å, º) top
N1—C6 | 1.3254 (19) | C44—N44 | 1.152 (2) |
N1—C2 | 1.338 (2) | C43—C45 | 1.361 (2) |
C2—N3 | 1.3184 (19) | C45—C51 | 1.434 (2) |
C2—O2 | 1.3495 (18) | C45—H45 | 0.9500 |
N3—C4 | 1.3593 (19) | C54—N54 | 1.363 (2) |
C4—C5 | 1.374 (2) | C51—C52 | 1.410 (2) |
C4—N41 | 1.3952 (19) | C52—C53 | 1.373 (2) |
C5—C6 | 1.396 (2) | C53—C54 | 1.418 (2) |
C5—H5 | 0.9500 | C54—C55 | 1.412 (2) |
C6—O6 | 1.3464 (18) | C55—C56 | 1.375 (2) |
O2—C21 | 1.4368 (19) | C56—C51 | 1.411 (2) |
C21—H21A | 0.9800 | C52—H52 | 0.9500 |
C21—H21B | 0.9800 | C53—H53 | 0.9500 |
C21—H21C | 0.9800 | C55—H55 | 0.9500 |
O6—C61 | 1.4463 (18) | C56—H56 | 0.9500 |
C61—H61A | 0.9800 | N54—C58 | 1.456 (2) |
C61—H61B | 0.9800 | N54—C57 | 1.457 (2) |
C61—H61C | 0.9800 | C57—H57A | 0.9800 |
N41—C42 | 1.372 (2) | C57—H57B | 0.9800 |
N41—H41 | 0.8800 | C57—H57C | 0.9800 |
C42—O42 | 1.2276 (18) | C58—H58A | 0.9800 |
C42—C43 | 1.489 (2) | C58—H58B | 0.9800 |
C43—C44 | 1.430 (2) | C58—H58C | 0.9800 |
| | | |
C6—N1—C2 | 114.06 (13) | N44—C44—C43 | 176.24 (17) |
N3—C2—N1 | 128.63 (14) | C43—C45—C51 | 132.50 (15) |
N3—C2—O2 | 119.29 (13) | C43—C45—H45 | 113.7 |
N1—C2—O2 | 112.06 (13) | C51—C45—H45 | 113.7 |
C2—N3—C4 | 114.77 (13) | C52—C51—C56 | 116.69 (14) |
N3—C4—C5 | 123.12 (14) | C52—C51—C45 | 125.07 (14) |
N3—C4—N41 | 112.10 (13) | C56—C51—C45 | 118.21 (14) |
C5—C4—N41 | 124.77 (14) | C53—C52—C51 | 121.59 (14) |
C4—C5—C6 | 114.85 (14) | C53—C52—H52 | 119.2 |
C4—C5—H5 | 122.6 | C51—C52—H52 | 119.2 |
C6—C5—H5 | 122.6 | C52—C53—C54 | 121.16 (15) |
N1—C6—O6 | 118.83 (13) | C52—C53—H53 | 119.4 |
N1—C6—C5 | 124.52 (14) | C54—C53—H53 | 119.4 |
O6—C6—C5 | 116.63 (13) | N54—C54—C55 | 121.37 (14) |
C2—O2—C21 | 116.88 (12) | N54—C54—C53 | 120.86 (15) |
O2—C21—H21A | 109.5 | C55—C54—C53 | 117.76 (14) |
O2—C21—H21B | 109.5 | C56—C55—C54 | 120.15 (14) |
H21A—C21—H21B | 109.5 | C56—C55—H55 | 119.9 |
O2—C21—H21C | 109.5 | C54—C55—H55 | 119.9 |
H21A—C21—H21C | 109.5 | C55—C56—C51 | 122.63 (15) |
H21B—C21—H21C | 109.5 | C55—C56—H56 | 118.7 |
C6—O6—C61 | 116.10 (12) | C51—C56—H56 | 118.7 |
O6—C61—H61A | 109.5 | C54—N54—C58 | 120.40 (14) |
O6—C61—H61B | 109.5 | C54—N54—C57 | 121.04 (13) |
H61A—C61—H61B | 109.5 | C58—N54—C57 | 118.42 (13) |
O6—C61—H61C | 109.5 | N54—C57—H57A | 109.5 |
H61A—C61—H61C | 109.5 | N54—C57—H57B | 109.5 |
H61B—C61—H61C | 109.5 | H57A—C57—H57B | 109.5 |
C42—N41—C4 | 127.57 (13) | N54—C57—H57C | 109.5 |
C42—N41—H41 | 116.2 | H57A—C57—H57C | 109.5 |
C4—N41—H41 | 116.2 | H57B—C57—H57C | 109.5 |
O42—C42—N41 | 122.18 (14) | N54—C58—H58A | 109.5 |
O42—C42—C43 | 121.69 (13) | N54—C58—H58B | 109.5 |
N41—C42—C43 | 116.12 (13) | H58A—C58—H58B | 109.5 |
C45—C43—C44 | 124.51 (14) | N54—C58—H58C | 109.5 |
C45—C43—C42 | 117.43 (14) | H58A—C58—H58C | 109.5 |
C44—C43—C42 | 118.04 (13) | H58B—C58—H58C | 109.5 |
| | | |
C6—N1—C2—N3 | −1.7 (2) | N41—C42—C43—C44 | 0.4 (2) |
C6—N1—C2—O2 | 179.81 (12) | C44—C43—C45—C51 | −3.6 (3) |
N1—C2—N3—C4 | 1.4 (2) | C42—C43—C45—C51 | 178.03 (15) |
O2—C2—N3—C4 | 179.79 (12) | C43—C45—C51—C52 | −8.9 (3) |
C2—N3—C4—C5 | 0.6 (2) | C43—C45—C51—C56 | 172.80 (15) |
C2—N3—C4—N41 | −178.15 (12) | N1—C2—O2—C21 | −178.19 (12) |
N3—C4—C5—C6 | −1.9 (2) | N1—C6—O6—C61 | −4.43 (19) |
N41—C4—C5—C6 | 176.64 (13) | C56—C51—C52—C53 | −1.2 (2) |
C2—N1—C6—O6 | 178.66 (12) | C45—C51—C52—C53 | −179.48 (14) |
C2—N1—C6—C5 | 0.1 (2) | C51—C52—C53—C54 | 0.2 (2) |
C4—C5—C6—N1 | 1.6 (2) | C52—C53—C54—N54 | −178.89 (14) |
C4—C5—C6—O6 | −177.02 (11) | C52—C53—C54—C55 | 0.7 (2) |
N3—C2—O2—C21 | 3.19 (19) | N54—C54—C55—C56 | 179.04 (14) |
C5—C6—O6—C61 | 174.28 (13) | C53—C54—C55—C56 | −0.6 (2) |
N3—C4—N41—C42 | −170.16 (13) | C54—C55—C56—C51 | −0.5 (2) |
C5—C4—N41—C42 | 11.1 (2) | C52—C51—C56—C55 | 1.4 (2) |
C4—N41—C42—O42 | 2.7 (2) | C45—C51—C56—C55 | 179.77 (14) |
C4—N41—C42—C43 | −177.93 (13) | C55—C54—N54—C58 | 1.5 (2) |
O42—C42—C43—C45 | −1.8 (2) | C55—C54—N54—C57 | 177.17 (13) |
N41—C42—C43—C45 | 178.81 (12) | C53—C54—N54—C57 | −3.2 (2) |
O42—C42—C43—C44 | 179.76 (13) | C53—C54—N54—C58 | −178.89 (13) |
(II) dimethylammonium 6-cyano-1,3-dimethyl-2,4,5-trioxo-1,2,3,4,5,8-
hexahydropyrido[2,3-
d]pyrimidin-8-ide
top
Crystal data top
C2H8N+·C10H7N4O3− | Z = 2 |
Mr = 277.29 | F(000) = 292 |
Triclinic, P1 | Dx = 1.415 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 8.1520 (5) Å | Cell parameters from 2419 reflections |
b = 9.2984 (8) Å | θ = 3.0–25.5° |
c = 9.7299 (8) Å | µ = 0.11 mm−1 |
α = 69.609 (3)° | T = 120 K |
β = 70.741 (4)° | Needle, yellow |
γ = 79.447 (5)° | 0.12 × 0.05 × 0.03 mm |
V = 650.69 (9) Å3 | |
Data collection top
Bruker Nonius KappaCCD area-detector diffractometer | 2419 independent reflections |
Radiation source: Bruker Nonius FR591 rotating anode | 1538 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.077 |
Detector resolution: 9.091 pixels mm-1 | θmax = 25.5°, θmin = 3.0° |
ϕ and ω scans | h = −9→9 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −11→11 |
Tmin = 0.988, Tmax = 0.997 | l = −11→11 |
9719 measured reflections | |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.065 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.194 | H-atom parameters constrained |
S = 1.03 | w = 1/[σ2(Fo2) + (0.1013P)2 + 0.2276P] where P = (Fo2 + 2Fc2)/3 |
2419 reflections | (Δ/σ)max = 0.001 |
185 parameters | Δρmax = 0.32 e Å−3 |
0 restraints | Δρmin = −0.33 e Å−3 |
Crystal data top
C2H8N+·C10H7N4O3− | γ = 79.447 (5)° |
Mr = 277.29 | V = 650.69 (9) Å3 |
Triclinic, P1 | Z = 2 |
a = 8.1520 (5) Å | Mo Kα radiation |
b = 9.2984 (8) Å | µ = 0.11 mm−1 |
c = 9.7299 (8) Å | T = 120 K |
α = 69.609 (3)° | 0.12 × 0.05 × 0.03 mm |
β = 70.741 (4)° | |
Data collection top
Bruker Nonius KappaCCD area-detector diffractometer | 2419 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 1538 reflections with I > 2σ(I) |
Tmin = 0.988, Tmax = 0.997 | Rint = 0.077 |
9719 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.065 | 0 restraints |
wR(F2) = 0.194 | H-atom parameters constrained |
S = 1.03 | Δρmax = 0.32 e Å−3 |
2419 reflections | Δρmin = −0.33 e Å−3 |
185 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.7706 (3) | 0.5365 (3) | 0.2930 (3) | 0.0241 (6) | |
C2 | 0.6987 (3) | 0.3996 (3) | 0.3378 (3) | 0.0247 (7) | |
N3 | 0.6587 (3) | 0.3176 (3) | 0.4918 (3) | 0.0244 (6) | |
C4 | 0.6821 (3) | 0.3648 (3) | 0.6056 (3) | 0.0231 (7) | |
C4a | 0.7570 (3) | 0.5110 (3) | 0.5526 (3) | 0.0216 (6) | |
C5 | 0.7927 (3) | 0.5721 (3) | 0.6572 (3) | 0.0217 (7) | |
C6 | 0.8678 (3) | 0.7188 (3) | 0.5836 (3) | 0.0243 (7) | |
C7 | 0.9031 (3) | 0.7888 (3) | 0.4276 (3) | 0.0258 (7) | |
H7 | 0.9533 | 0.8849 | 0.3855 | 0.031* | |
N8 | 0.8717 (3) | 0.7306 (3) | 0.3307 (3) | 0.0263 (6) | |
C8a | 0.8015 (3) | 0.5946 (3) | 0.3955 (3) | 0.0219 (7) | |
C11 | 0.8251 (4) | 0.6202 (4) | 0.1281 (3) | 0.0329 (8) | |
H11A | 0.9525 | 0.6114 | 0.0896 | 0.049* | |
H11B | 0.7832 | 0.7289 | 0.1111 | 0.049* | |
H11C | 0.7758 | 0.5760 | 0.0739 | 0.049* | |
O2 | 0.6683 (3) | 0.3502 (3) | 0.2480 (2) | 0.0342 (6) | |
C31 | 0.5889 (4) | 0.1671 (4) | 0.5392 (4) | 0.0349 (8) | |
H31A | 0.5234 | 0.1689 | 0.4703 | 0.052* | |
H31B | 0.5115 | 0.1450 | 0.6442 | 0.052* | |
H31C | 0.6854 | 0.0870 | 0.5346 | 0.052* | |
O4 | 0.6390 (3) | 0.2813 (2) | 0.7386 (2) | 0.0310 (5) | |
O5 | 0.7642 (2) | 0.5067 (2) | 0.7990 (2) | 0.0263 (5) | |
C61 | 0.9088 (4) | 0.7896 (3) | 0.6770 (3) | 0.0260 (7) | |
N61 | 0.9408 (3) | 0.8469 (3) | 0.7516 (3) | 0.0363 (7) | |
N21 | 0.6842 (3) | 0.2360 (3) | 1.0197 (3) | 0.0257 (6) | |
H21A | 0.7156 | 0.2781 | 1.0792 | 0.031* | |
H21B | 0.6964 | 0.3082 | 0.9247 | 0.031* | |
C22 | 0.4996 (4) | 0.2018 (4) | 1.0896 (4) | 0.0328 (8) | |
H22A | 0.4842 | 0.1291 | 1.1931 | 0.049* | |
H22B | 0.4652 | 0.1564 | 1.0271 | 0.049* | |
H22C | 0.4268 | 0.2972 | 1.0949 | 0.049* | |
C23 | 0.8040 (4) | 0.0987 (4) | 1.0028 (4) | 0.0330 (8) | |
H23A | 0.7690 | 0.0510 | 0.9425 | 0.050* | |
H23B | 0.7990 | 0.0247 | 1.1043 | 0.050* | |
H23C | 0.9232 | 0.1296 | 0.9505 | 0.050* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0261 (12) | 0.0285 (15) | 0.0181 (13) | −0.0035 (10) | −0.0082 (10) | −0.0053 (11) |
C2 | 0.0214 (14) | 0.0283 (18) | 0.0251 (17) | −0.0007 (12) | −0.0070 (12) | −0.0097 (14) |
N3 | 0.0281 (13) | 0.0241 (14) | 0.0226 (14) | −0.0056 (10) | −0.0075 (10) | −0.0073 (11) |
C4 | 0.0201 (14) | 0.0275 (17) | 0.0228 (17) | −0.0001 (12) | −0.0062 (12) | −0.0099 (14) |
C4a | 0.0197 (14) | 0.0222 (16) | 0.0213 (16) | 0.0005 (11) | −0.0044 (12) | −0.0073 (13) |
C5 | 0.0188 (13) | 0.0244 (17) | 0.0218 (17) | 0.0021 (11) | −0.0055 (12) | −0.0092 (13) |
C6 | 0.0222 (14) | 0.0250 (17) | 0.0243 (17) | −0.0022 (12) | −0.0048 (12) | −0.0075 (13) |
C7 | 0.0238 (14) | 0.0216 (17) | 0.0302 (18) | −0.0020 (12) | −0.0077 (13) | −0.0057 (14) |
N8 | 0.0276 (13) | 0.0257 (15) | 0.0241 (14) | −0.0045 (10) | −0.0075 (10) | −0.0047 (11) |
C8a | 0.0179 (13) | 0.0248 (17) | 0.0231 (16) | 0.0021 (11) | −0.0072 (12) | −0.0080 (13) |
C11 | 0.0435 (18) | 0.036 (2) | 0.0198 (17) | −0.0058 (15) | −0.0098 (14) | −0.0073 (14) |
O2 | 0.0409 (12) | 0.0422 (14) | 0.0281 (12) | −0.0078 (10) | −0.0130 (10) | −0.0161 (11) |
C31 | 0.0473 (19) | 0.0296 (19) | 0.0316 (19) | −0.0102 (15) | −0.0124 (15) | −0.0094 (15) |
O4 | 0.0416 (12) | 0.0280 (13) | 0.0232 (13) | −0.0109 (9) | −0.0092 (10) | −0.0037 (10) |
O5 | 0.0336 (11) | 0.0249 (12) | 0.0213 (12) | −0.0029 (9) | −0.0086 (9) | −0.0074 (9) |
C61 | 0.0242 (15) | 0.0236 (17) | 0.0268 (17) | −0.0048 (12) | −0.0031 (12) | −0.0062 (14) |
N61 | 0.0474 (17) | 0.0320 (17) | 0.0312 (16) | −0.0136 (13) | −0.0088 (13) | −0.0091 (13) |
N21 | 0.0319 (13) | 0.0265 (15) | 0.0189 (13) | −0.0050 (11) | −0.0069 (10) | −0.0064 (11) |
C22 | 0.0297 (16) | 0.037 (2) | 0.0301 (18) | −0.0042 (13) | −0.0070 (14) | −0.0095 (15) |
C23 | 0.0319 (16) | 0.0292 (19) | 0.0333 (19) | 0.0021 (14) | −0.0079 (14) | −0.0078 (15) |
Geometric parameters (Å, º) top
N1—C2 | 1.368 (4) | C7—H7 | 0.9500 |
C2—N3 | 1.381 (4) | C11—H11A | 0.9800 |
N3—C4 | 1.401 (3) | C11—H11B | 0.9800 |
C4—C4a | 1.447 (4) | C11—H11C | 0.9800 |
C4a—C5 | 1.449 (4) | C31—H31A | 0.9800 |
C5—C6 | 1.444 (4) | C31—H31B | 0.9800 |
C6—C7 | 1.379 (4) | C31—H31C | 0.9800 |
C7—N8 | 1.346 (4) | N21—C22 | 1.476 (4) |
N8—C8a | 1.340 (4) | N21—C23 | 1.481 (4) |
C8a—N1 | 1.393 (4) | N21—H21A | 0.9200 |
C4a—C8a | 1.408 (4) | N21—H21B | 0.9200 |
N1—C11 | 1.470 (4) | C22—H22A | 0.9800 |
C2—O2 | 1.225 (3) | C22—H22B | 0.9800 |
N3—C31 | 1.471 (4) | C22—H22C | 0.9800 |
C4—O4 | 1.225 (4) | C23—H23A | 0.9800 |
C5—O5 | 1.258 (3) | C23—H23B | 0.9800 |
C6—C61 | 1.438 (4) | C23—H23C | 0.9800 |
C61—N61 | 1.151 (4) | | |
| | | |
C2—N1—C8a | 122.8 (2) | H11A—C11—H11B | 109.5 |
C2—N1—C11 | 117.6 (2) | N1—C11—H11C | 109.5 |
C8a—N1—C11 | 119.5 (2) | H11A—C11—H11C | 109.5 |
O2—C2—N1 | 122.8 (3) | H11B—C11—H11C | 109.5 |
O2—C2—N3 | 120.3 (3) | N3—C31—H31A | 109.5 |
N1—C2—N3 | 117.0 (2) | N3—C31—H31B | 109.5 |
C2—N3—C4 | 125.4 (2) | H31A—C31—H31B | 109.5 |
C2—N3—C31 | 117.0 (2) | N3—C31—H31C | 109.5 |
C4—N3—C31 | 117.6 (2) | H31A—C31—H31C | 109.5 |
O4—C4—N3 | 118.6 (3) | H31B—C31—H31C | 109.5 |
O4—C4—C4a | 125.9 (3) | N61—C61—C6 | 179.6 (3) |
N3—C4—C4a | 115.6 (2) | C22—N21—C23 | 113.3 (2) |
C8a—C4a—C4 | 119.7 (2) | C22—N21—H21A | 108.9 |
C8a—C4a—C5 | 118.8 (3) | C23—N21—H21A | 108.9 |
C4—C4a—C5 | 121.5 (2) | C22—N21—H21B | 108.9 |
O5—C5—C6 | 121.3 (2) | C23—N21—H21B | 108.9 |
O5—C5—C4a | 125.0 (3) | H21A—N21—H21B | 107.7 |
C6—C5—C4a | 113.6 (2) | N21—C22—H22A | 109.5 |
C7—C6—C61 | 120.4 (3) | N21—C22—H22B | 109.5 |
C7—C6—C5 | 121.4 (3) | H22A—C22—H22B | 109.5 |
C61—C6—C5 | 118.2 (2) | N21—C22—H22C | 109.5 |
N8—C7—C6 | 124.7 (3) | H22A—C22—H22C | 109.5 |
N8—C7—H7 | 117.6 | H22B—C22—H22C | 109.5 |
C6—C7—H7 | 117.6 | N21—C23—H23A | 109.5 |
C8a—N8—C7 | 115.4 (2) | N21—C23—H23B | 109.5 |
N8—C8a—N1 | 114.4 (2) | H23A—C23—H23B | 109.5 |
N8—C8a—C4a | 126.1 (3) | N21—C23—H23C | 109.5 |
N1—C8a—C4a | 119.6 (3) | H23A—C23—H23C | 109.5 |
N1—C11—H11A | 109.5 | H23B—C23—H23C | 109.5 |
N1—C11—H11B | 109.5 | | |
| | | |
C8a—N1—C2—O2 | 178.4 (2) | C4—C4a—C5—C6 | 179.8 (2) |
C11—N1—C2—O2 | −4.8 (4) | O5—C5—C6—C7 | 178.4 (2) |
C8a—N1—C2—N3 | −0.9 (4) | C4a—C5—C6—C7 | −1.1 (4) |
C11—N1—C2—N3 | 175.9 (2) | O5—C5—C6—C61 | −0.4 (4) |
O2—C2—N3—C4 | −177.8 (2) | C4a—C5—C6—C61 | −179.8 (2) |
N1—C2—N3—C4 | 1.5 (4) | C61—C6—C7—N8 | 179.1 (2) |
O2—C2—N3—C31 | 3.4 (4) | C5—C6—C7—N8 | 0.4 (4) |
N1—C2—N3—C31 | −177.2 (2) | C6—C7—N8—C8a | −0.2 (4) |
C2—N3—C4—O4 | 179.2 (2) | C7—N8—C8a—N1 | −179.8 (2) |
C31—N3—C4—O4 | −2.1 (4) | C7—N8—C8a—C4a | 0.9 (4) |
C2—N3—C4—C4a | −0.9 (4) | C2—N1—C8a—N8 | −179.6 (2) |
C31—N3—C4—C4a | 177.8 (2) | C11—N1—C8a—N8 | 3.7 (4) |
O4—C4—C4a—C8a | 179.6 (2) | C2—N1—C8a—C4a | −0.3 (4) |
N3—C4—C4a—C8a | −0.3 (4) | C11—N1—C8a—C4a | −177.0 (2) |
O4—C4—C4a—C5 | 1.5 (4) | C4—C4a—C8a—N8 | −179.9 (2) |
N3—C4—C4a—C5 | −178.4 (2) | C5—C4a—C8a—N8 | −1.7 (4) |
C8a—C4a—C5—O5 | −177.8 (2) | C4—C4a—C8a—N1 | 0.8 (4) |
C4—C4a—C5—O5 | 0.4 (4) | C5—C4a—C8a—N1 | 179.0 (2) |
C8a—C4a—C5—C6 | 1.6 (3) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N21—H21A···O2i | 0.92 | 1.88 | 2.735 (4) | 153 |
N21—H21B···O4 | 0.92 | 2.12 | 2.757 (3) | 126 |
N21—H21B···O5 | 0.92 | 1.89 | 2.699 (3) | 146 |
C7—H7···N61ii | 0.95 | 2.54 | 3.483 (4) | 172 |
Symmetry codes: (i) x, y, z+1; (ii) −x+2, −y+2, −z+1. |
Experimental details
| (I) | (II) |
Crystal data |
Chemical formula | C18H19N5O3 | C2H8N+·C10H7N4O3− |
Mr | 353.38 | 277.29 |
Crystal system, space group | Triclinic, P1 | Triclinic, P1 |
Temperature (K) | 120 | 120 |
a, b, c (Å) | 7.9772 (2), 10.0023 (4), 10.8409 (5) | 8.1520 (5), 9.2984 (8), 9.7299 (8) |
α, β, γ (°) | 93.693 (2), 93.562 (3), 99.196 (2) | 69.609 (3), 70.741 (4), 79.447 (5) |
V (Å3) | 849.80 (6) | 650.69 (9) |
Z | 2 | 2 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.10 | 0.11 |
Crystal size (mm) | 0.23 × 0.12 × 0.12 | 0.12 × 0.05 × 0.03 |
|
Data collection |
Diffractometer | Bruker Nonius KappaCCD area-detector diffractometer | Bruker Nonius KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.978, 0.988 | 0.988, 0.997 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 15270, 3350, 2512 | 9719, 2419, 1538 |
Rint | 0.055 | 0.077 |
(sin θ/λ)max (Å−1) | 0.618 | 0.606 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.047, 0.133, 1.04 | 0.065, 0.194, 1.03 |
No. of reflections | 3350 | 2419 |
No. of parameters | 239 | 185 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.30, −0.28 | 0.32, −0.33 |
Selected geometric parameters (Å, º) for (I) topC42—O42 | 1.2276 (18) | C51—C52 | 1.410 (2) |
C42—C43 | 1.489 (2) | C52—C53 | 1.373 (2) |
C43—C44 | 1.430 (2) | C53—C54 | 1.418 (2) |
C44—N44 | 1.152 (2) | C54—C55 | 1.412 (2) |
C43—C45 | 1.361 (2) | C55—C56 | 1.375 (2) |
C45—C51 | 1.434 (2) | C56—C51 | 1.411 (2) |
C54—N54 | 1.363 (2) | | |
| | | |
N3—C4—N41—C42 | −170.16 (13) | N1—C2—O2—C21 | −178.19 (12) |
C4—N41—C42—C43 | −177.93 (13) | N1—C6—O6—C61 | −4.43 (19) |
N41—C42—C43—C45 | 178.81 (12) | C53—C54—N54—C57 | −3.2 (2) |
C42—C43—C45—C51 | 178.03 (15) | C53—C54—N54—C58 | −178.89 (13) |
C43—C45—C51—C52 | −8.9 (3) | | |
Selected bond lengths (Å) for (II) topN1—C2 | 1.368 (4) | N8—C8a | 1.340 (4) |
C2—N3 | 1.381 (4) | C8a—N1 | 1.393 (4) |
N3—C4 | 1.401 (3) | C4a—C8a | 1.408 (4) |
C4—C4a | 1.447 (4) | C2—O2 | 1.225 (3) |
C4a—C5 | 1.449 (4) | C4—O4 | 1.225 (4) |
C5—C6 | 1.444 (4) | C5—O5 | 1.258 (3) |
C6—C7 | 1.379 (4) | C6—C61 | 1.438 (4) |
C7—N8 | 1.346 (4) | C61—N61 | 1.151 (4) |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N21—H21A···O2i | 0.92 | 1.88 | 2.735 (4) | 153 |
N21—H21B···O4 | 0.92 | 2.12 | 2.757 (3) | 126 |
N21—H21B···O5 | 0.92 | 1.89 | 2.699 (3) | 146 |
C7—H7···N61ii | 0.95 | 2.54 | 3.483 (4) | 172 |
Symmetry codes: (i) x, y, z+1; (ii) −x+2, −y+2, −z+1. |
We report here the structures of the title compounds, (I) and (II) (Figs. 1 and 2), which result from the reactions of cyanoacetylpyrimidine derivatives with, respectively, 4-dimethylaminobenzaldehyde (Quiroga et al., 2009; see first scheme) and dimethylformamide dimethylacetal (see second scheme). The use of 5-cyanoacetylpyrimidines as intermediates for the synthesis of substituted pyrido[2,3-d]pyrimidin-5-ones has recently been described (Quiroga et al., 2009), and compounds (I) and (II), for which structures are reported here, were both synthesized using variations of the recently reported procedure.
Within the molecule of (I) (Fig. 1), the spacer unit linking the two rings adopts an all-trans configuration which is nearly planar, while the two rings are each twisted out of this plane by less than 10°, as shown by the leading torsion angles (Table 1). Similarly, the C atoms of the methoxy groups are almost coplanar with the adjacent pyrimidine ring, with deviations from the ring plane of 0.071 (2) Å for atom C21 and 0.195 (2) Å for atom C61, although the spatial disposition of these groups differs from that originally suggested (Quiroga et al., 2009).
The bond distances in the molecule of (I) show some values which are worthy of comment (Table 1). In the C51–C56 aryl ring, the two bonds C52—C53 and C55—C56 are significantly shorter than the other four bonds; the exocyclic C54—N54 bond is somewhat short for its type [mean value (Allen et al., 1987) 1.371 Å]; the C45—C51 bond is very short for its type (mean value 1.470 Å, lower quartile value 1.463 Å), while the C43—C45 bond is long for its type (mean value 1.326 Å, upper quartile value 1.334 Å). Although the C42—C43 and C42—O42 bonds have lengths typical of their types, the C43—C44 bond is shorter than those found in a series of analogous nitriles where electronic conjugation is not possible [mean value 1.442 (4) Å; Cobo et al., 2005, 2006, 2009] and the C44—N44 bond is correspondingly longer [mean value 1.130 (4) Å]. Thus, within the spacer unit, the bond-length anomalies are concentrated in the carbonitrile fragment, rather than in the carbonyl fragment and its adjacent C—C bonds. Taken as a whole, the bond distances in (I) indicate that form (Ia) (see first scheme), which is intuitively the more obvious of the polarized forms, probably makes only a very small contribution to the overall electronic structure, while form (Ib) is a significant contributor, in addition to the classical unpolarized form (I).
In the anion of compound (II) (Fig. 2), it is striking that, while the C2—O2 and C4—O4 distances are identical and typical of their type, the C5—O5 distance is significantly longer (Table 2). As found for the analogous bonds in (I), the C6—C61 bond in (II) is slightly short for its type and C61—N61 is slightly long. Thus, the forms (IIa) and, to a lesser extent, (IIb) are contributors to the overall electronic structure, in addition to the simple form (II) (see second scheme).
Despite the polarization of the electronic structure in (I), neither atom O42 nor N44 acts as a hydrogen-bond acceptor. Indeed, there are no hydrogen bonds of any kind in the crystal structure of (I). In particular, the N—H unit does not act as a hydrogen-bond donor, as the nearest potential hydrogen-bond acceptor is atom O42 in the molecule at (1 - x, 1 - y, 1 - z) and the geometric parameters for this contact are N41···O42i = 3.501 (2) Å, H41···O42i = 3.51 Å and N41—H41···O42i = 82° [symmetry code: (i) 1 - x, 1 y, 1 - z]. Nor are there any N—H···π or C—H···π hydrogen bonds present. Instead, pairs of molecules related by inversion are linked into centrosymmetric dimers (Fig. 3) by a single π–π stacking interaction. The aryl ring of the molecule at (x, y, z) and the pyrimidine ring of the molecule at (1 - x, 1 - y, 1 - z) make a dihedral angle of only 2.2 (2)°. The corresponding ring-centroid separation is 3.632 (2) Å and the interplanar spacing is ca 3.395 Å, with a ring-centroid offset of ca 1.29 Å. There are no direction-specific interactions between these dimers.
In compound (II), the ionic components in the selected asymmetric unit are linked by a slightly asymmetric but nonetheless planar three-centre N—H···(O)2 hydrogen bond (Table 3, Fig. 2), forming an R12(6) motif (Bernstein et al., 1995). The shorter component of this three-centre system involves atom O5 as the acceptor and, because of the polarization in form (IIa), this stronger component could be regarded as a charge-assisted hydrogen bond (Gilli et al., 1994). In addition, atom N21 in the cation at (x, y, z) acts as hydrogen-bond donor to atom O2 in the anion at (x, y, 1 + z), and the combination of all the N—H···O interactions generates a hydrogen-bonded C22(8)C22(10)[R12(6)] chain of rings (Fig. 4). Finally, a single C—H···N hydrogen bond, which utilizes the nitrile N atom as the acceptor, links an antiparallel pair of chains of rings into a ribbon running parallel to the [001] direction in which R22(10) rings centred at (1, 1, 1/2 + n), where n represents an integer, alternate with R66(30) rings centred at (1, 1, n), where n again represents an integer (Fig. 4). There are no direction-specific interactions between adjacent ribbons.
The formation of the salt (II) in the reaction of dimethylformamide dimethylacetal with a cyanoacetylpyrimidine derivative may be contrasted with the reaction (Galvez et al., 2008) of the same acetal with a cyanoacetylindole derivative to form the neutral compound, (III) (see third scheme). Here, the intramolecular distances indicate that both of the polarized forms, (IIIa) and (IIIb), are significant contributors to the overall electronic structure. The formation of these compounds, and of (I), attests to the synthetic versatility of cyanoacetyl derivatives as intermediates for the synthesis of new heterocyclic compounds.